anno_eset | Annotating gene expression matrix and remove duplicated genes |
assimilate_data | Assimilate data with similar columns |
batch_cor | Batch to conduct correlation analysis with multiple features |
batch_kruskal | batch_kruskal |
batch_pcc | Batch way to calculate the partial correlation coefficient |
batch_sig_surv_plot | Title |
batch_surv | batch_surv - Batch Survival Analysis Function |
batch_wilcoxon | Batch to conduct wilcoxon test between two groups |
best_cutoff | Extract best cut-off and add new binary object to data frame |
best_cutoff2 | Extract best cut-off and add new binary object to data frame |
BinomialAUC | BinomialAUC |
BinomialModel | Binomial Model construction |
break_month | break month |
CalculatePref | Calculate Pref |
calculate_sig_score | Calculating signature score on a gene expression dataset |
calculate_sig_score_integration | Calculating signature score using Integration method |
calculate_sig_score_pca | Calculating signature score using PCA method |
calculate_sig_score_ssgsea | Calculating signature score using ssGSEA method |
calculate_sig_score_zscore | Calculating signature score using z-score method |
CalculateTimeROC | Calculate Time ROC |
cell_bar_plot | Visualize the results as a stacked bar chart with... |
check_cancer_types | process batch table and check cancer types. |
check_eset | check_eset - Check integrity and outliers of expression set |
CIBERSORT | CIBERSORT is an analytical tool developed by Newman et al. to... |
combine_pd_eset | Title combine_pd_eset |
Construct_con | Construct contrast |
ConvertRownameToLoci | Convert Rowname To Loci |
CoreAlg | Title CoreAlg |
count2tpm | Convert read counts to transcripts per million (TPM) |
creat_folder | Title creates a new folder or directory |
deconvo_cibersort | Decoding immune microenvironment using CIBERSORT |
deconvo_epic | Estimating immune microenvironment using EPIC: FOR RNAseq... |
deconvo_estimate | Calculation of stromal, immune, and ESTIMATE scores |
deconvo_ips | Calculating immune phenotype score using IPS |
deconvolute_quantiseq.default | Use quanTIseq to deconvolute a gene expression matrix. |
deconvolute_timer.default | deconvolute tumor microenvironment using timer |
deconvo_mcpcounter | Estimating immune microenvironment using MCP-counter |
deconvo_quantiseq | Deconvoluting micrornvironment using the quanTIseq technique |
deconvo_ref | Estimate the fraction of cell types using defined reference... |
deconvo_timer | Deconvoluting using the TIMER technique Unlike the other... |
deconvo_tme | Deconvoluting Tumor microenvironment on a transcriptomic... |
deconvo_xcell | Decoding immune microenvironment using xCell |
design_mytheme | design_mytheme |
doPerm | Title |
DrawQQPlot | Draw QQ Plot |
Enet | Enet |
enrichment_barplot | Enrichment bar plot with two directions |
EPIC | Estimate the proportion of immune and cancer cells. |
eset_distribution | Title eset_distribution |
estimateScore | estimateScore |
exact_pvalue | Calculate exact p value of correlation |
extract_sc_data | Extract data frame |
feature_manipulation | feature_manipulation - Manipulate features in a matrix or... |
feature_select | Feature selection |
filterCommonGenes | filterCommonGenes |
find_markers_in_bulk | Find markers in bulk |
find_mutations | Searching for mutations related to signature score |
find_outlier_samples | Identification of Potential Outlier Samples in Gene... |
find_variable_genes | Title find_variable_genes |
format_msigdb | Format input signatures from MsgiDB |
format_signatures | Transform signature gene data into list format |
generateRef | Generate Reference signature matrix |
generateRef_DEseq2 | Generate Reference signature matrix using DEseq2 |
generateRef_limma | Generate Reference signature matrix using limma |
generateRef_rnaseq | Generate reference gene matrix from DEGs result |
generateRef_seurat | generateRef_seurat |
get_cols | Set and view the color palettes |
get_cor | Calculate and Visualize Correlation between Two Variables |
get_cor_matrix | Calculate and Visualize Correlation Matrix between Two... |
GetFractions.Abbas | Constrained regression method implemented in Abbas et al.,... |
getHRandCIfromCoxph | Extract hazard ratio and confidence intervals from a coxph... |
GetOutlierGenes | Get Outlier Genes |
get_sig_sc | get_sig_sc |
high_var_fea | Extract most variable features form statistical results |
iobr_cor_plot | Integrative correlation between phenotype and features |
iobr_deconvo_pieline | Title iobr_deconvo_pieline |
iobr_deg | iobr_deg |
iobr_pca | Principal Component Analysis (PCA) Visualization |
IPS_calculation | This R-script can be used to calculate Immunophenoscore (IPS) |
ipsmap | Title |
lasso_select | Constructing predictive or prognostic model |
limma.dif | Title |
log2eset | Judge whether the expression set needs log2 transformation |
LR_cal | LR_cal |
make_mut_matrix | Make mutation matrix using maf data |
mapbw | Title |
mapcolors | Title |
merge_duplicate | Merge data frames with duplicated column names |
merge_duplicates | Merging the duplicates from the input matrix. |
merge_eset | Merge expression sets by row names |
microenvironmentScores | Calculate microenvironment scores |
mouse2human_eset | Converting mouse gene symbol to human gene symbol of... |
outputGCT | outputGCT |
output_sig | save signature data into a data frame |
palettes | Choose colors. |
ParseInputExpression | Input gene expression |
percent_bar_plot | Function to create a percent bar plot. |
pie_chart | pie_chart |
PlotAUC | Plot AUC |
plotPurity | plotPurity |
PlotTimeROC | Plot Time ROC |
ProcessingData | Processing Data |
PrognosticAUC | Prognostic AUC |
PrognosticModel | Prognostic Model construction |
PrognosticResult | Prognostic Result |
quantiseq_helper | Helper functions for quanTIseq |
rawEnrichmentAnalysis | Calculated raw xCell enrichment scores |
rbind_iobr | rbind_iobr |
RegressionResult | Regression Result |
remove_batcheffect | Removing batch effect of two or three expression set |
RemoveBatchEffect | Remove batch effect of expression set |
remove_duplicate_genes | Remove duplicate gene symbol on a gene expression data |
remove_names | Batch to transform patterns to special character |
roc_time | roc_time |
scaleCounts | Scaling raw counts from each sample. |
scale_matrix | scale_matrix - Scale and manipulate a matrix |
select_method | Choose which method to conduct following analysis |
sig_box | Title: sig_box - Generate a Box plot with Statistical... |
sig_box_batch | Title sig_box_batch |
sig_forest | Forest plot of survival analysis results. |
sig_gsea | sig_gsea - Perform Gene Set Enrichment Analysis |
sig_heatmap | sig_heatmap |
signature_score_calculation_methods | List of supported signature score calculation methods |
sig_pheatmap | Title sig_pheatmap |
sig_roc | Drawing multiple AUC into one graph |
sigScore | Calculate siganture score using PCA function |
sig_surv_plot | Multiple survival KM-plot to a signature or gene |
spillOver | Adjust scores using the spillover compensation method |
SplitTrainTest | Split Train and Test data |
subgroup_survival | Title Extract hazard ratio and confidence intervals from a... |
surv_group | Drawing KM-plot to a Categorical variable with two or more... |
tcga_rna_preps | Title tcga_rna_preps |
timer_available_cancers | TIMER signatures are cancer specific. This is the list of... |
TimerINFO | Source code for the TIMER deconvolution method. |
tme_cluster | tme_cluster |
tme_deconvolution_methods | Collection of tumor microenvironment cell fraction... |
Top_probe | Top probe |
transform_data | Transform features with Inf or NA to other number |
transformScores | Transform scores from raw scores to fractions |
xCellAnalysis | The xCell analysis pipeline |
xCellSignifcanceBetaDist | Calculate significance p-values for the null hypothesis that... |
xCellSignifcanceRandomMatrix | Calculate significance p-values for the null hypothesis that... |
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